A facile PDMS–glass hybrid microfluidic device is developed for generating uniform submicrometer-scale double emulsion droplets with unprecedented simplicity and controllability. Compared with planar flow-focusing geometries, our three-dimensional flow-focusing geometry is advantageous for stably producing femto- to atto-liter droplets without the retraction problem of the dispersed phase fluid. In addition, this microfluidic platform can withstand the use of strong organic solvents (e.g. tetrahydrofuran (THF) and toluene) as a dispersed phase without deforming PDMS devices because the dispersed phase containing organic solvents does not directly contact the PDMS wall. In particular, monodisperse double emulsions are generated spontaneously via the internal phase separation of single emulsions driven by the diffusion of a co-solvent (tetrahydrofuran) in microfluidic devices. Finally, we demonstrated that the double emulsions can be used as morphological templates of ultrafine spherical silica capsules with controlled hierarchical pore networks via the evaporation-induced self-assembly (EISA) method. During EISA, triblock copolymers (Pluronic F127) act as a surfactant barrier separating the internal droplet from the continuous oil phase, resulting in the ‘inverse’ morphology (i.e. hydrophobic polymer-in-water-in-oil emulsions). Depending on the precursor composition and kinetic condition, various structural and morphological features, such as mesoporous hollow silica spheres with a single central core, multi-cores, or a combination of these with robust controllability can be seen. Electron microscopy (SEM, STEM, HR-TEM), small angle X-ray scattering (SAXS), and N2 adsorption–desorption confirm the well-controlled hierarchical pore structure of the resulting particles.